[Psidev-pi-dev] unimod.obo and XSLT

[Martin E. <mar...@ru...>]

Hi all!

To report modifications of resulting peptides we want to use unimod.

I assembled a XSLT to transform the XML from
http://www.unimod.org/xml/unimod.xml
to a unimod.obo (e.g. with XMLSpy).

For each (modification,specificity) pair an OBO term was created
(technically: a (umod:mod,spec_group) pair was transformed into a term with 
a unique accession. For XSLT simplicity the accessions were created as
"PI-UNIMOD:"+record_id+"0"+spec_group, which creates gaps between
accession numbers, but ensures uniqueness).

Only the umod:xref elements PMID, RESID and FindMod are transformed to Dbxrefs in 
obo; some of them had an invalid type in the XML, which I corrected
(I will report these to the unimod people).

Other umod:xrefs like "Misc. URL", "Book" or "Other" can be transformed
to property_values later.

I added unimod.obo and unimodXML2OBO.xsl 
to http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv

Hope that helps...

 Bye
   Martin